In the first episode, "Federation", the Vardaine turn against Dr. Bredell very quickly. This is due to the fact that his plan is insane. Yes, they can destroy the Federation by blowing up Earth but the rest of the worlds will undoubtedly descend on their homeworld quickly. Building Constitution-class ships is one thing. Genocide with a questionable weapon is another. He's also a Bad Boss that everyone hates.
In the second episode, "Sentinel", the team encounters a computer containing vast amounts of data on advanced holographic technology - which later turns out to have been placed there by the Brassica. We also see some use of holography in "Light and Darkness", with Azrael, Vizznr and Cicissa who are intelligent, reactive holograms. This pays off later on, when the utter weirdness of the alien ship in "Though This Be Madness" can entirely be explained by the ship (or at least its interiors) being a hologram, including every single one of its passengers. This may also have been cleverly foreshadowed by Trelane's fictional town of Gothos, which is also entirely fictional (though its residents, in that case, are at least physically real).
In the third episode, "No Man's Land", Kirk can't actually horrify Trelane with all the evil done in WW1. He's a vastly intelligent being with little empathy after all. No, what Kirk does is make it boring by saying his reproduction is stupid and hack work.
In the fourth episode, "Light and Darkness", Kirk's argument that the Alphans and Omegans are neither good nor evil because they're single-celled organisms seems to be a contrast to the Beauty Equals Goodness aesop being told. However, he's recognizing the Brassici are transparently manipulating them via a ridiculous moral binary. Neither side is actually sentient so the whole "test" they're being put through of looking past appearances is meaningless.
If you get killed or captured during "Federation", you're treated to a cutscene showing Breddell's doomsday weapon firing at Earth and blowing it apart - with the U.S.S. Alexander blown clear from the explosion, causing it to travel back in time to meet the Enterprise again. This indicates that the Alexander was in Earth's orbit when the explosion occurred, and traveled back in time from that location. However, Kirk's Captain's Log recorded after the encounter indicates that they've "traced the Alexander's course back to Espoir Station", which makes no sense: The Alexander didn't come from Espoir Station; it came from Earth.
